changeset 51:52cf1f7f11c5 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_ppfun.xml	Fri Feb 22 11:12:11 2019 -0500
@@ -0,0 +1,41 @@
+<tool id="minfi_ppfun" name="Minfi Preprocess Funnorm" version="@MINFI_VERSION@">
+    <description>implements the functional normalization algorithm</description><macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement>
+    </expand>
+    <command detect_errors="exit_code">
+    <![CDATA[
+     Rscript '$minfi_pp_script'
+    ]]>
+    </command>
+    <configfiles>
+    <configfile name="minfi_pp_script"><![CDATA[
+require("minfi", quietly = TRUE)
+RGSet <- get(load('$rgset'))
+
+GRSet <- preprocessFunnorm(RGSet)
+
+save(GRSet,file = '$grset')
+ ]]> 
+    </configfile>
+    </configfiles> 
+
+<inputs>
+        <param type="data" name="rgset" format="rdata" label="RGChannelSet" help="These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array." />
+    </inputs>
+    <outputs>
+        <data name="grset" format="rdata" label="GenomicRatioSet"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="rgset" value="RGChannelSet.rdata"/>
+            <output name="grset" file="FunGenomicRatioSet.rdata"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        This tool uses the internal control probes present on the array to infer between-array technical variation. It is particularly useful for studies comparing conditions with known large-scale differences, such as cancer/normal studies, or between-tissue studies. It has been shown that for such studies, functional normalization outperforms other existing approaches (Jean-Philippe Fortin et al. 2014).
+    ]]></help>
+    <expand macro="citations" />
+</tool>